import_pyrotagger_tab.Rd 2.98 KB
 Andreas Tille committed Sep 22, 2017 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 % Generated by roxygen2: do not edit by hand % Please edit documentation in R/IO-methods.R \name{import_pyrotagger_tab} \alias{import_pyrotagger_tab} \title{Imports a tab-delimited version of the pyrotagger output file.} \usage{ import_pyrotagger_tab(pyrotagger_tab_file, strict_taxonomy=FALSE, keep_potential_chimeras=FALSE) } \arguments{ \item{pyrotagger_tab_file}{(Required). A character string. The name of the tab-delimited pyrotagger output table.} \item{strict_taxonomy}{(Optional). Logical. Default \code{FALSE}. Should the taxonomyTable component be limited to just taxonomic data? Default includes all fields from the pyrotagger file.} \item{keep_potential_chimeras}{(Optional). Logical. Default \code{FALSE}. The pyrotagger output also includes OTUs that are tagged by pyrotagger as likely chimeras. These putative chimeric OTUs can be retained if set to \code{TRUE}. The putative chimeras are excluded by default.} } \value{ An \code{otuTax} object containing both the otu_table and TaxonomyTable data components, parsed from the pyrotagger output. } \description{ PyroTagger is a web-server that takes raw, barcoded 16S rRNA amplicon sequences and returns an excel spreadsheet (\code{".xls"}) with both abundance and taxonomy data. It also includes some confidence information related to the taxonomic assignment. } \details{ PyroTagger is created and maintained by the Joint Genome Institute at \code{"http://pyrotagger.jgi-psf.org/"} The typical output form PyroTagger is a spreadsheet format \code{".xls"}, which poses additional import challenges. However, virtually all spreadsheet applications support the \code{".xls"} format, and can further export this file in a tab-delimited format. It is recommended that you convert the xls-file without any modification (as tempting as it might be once you have loaded it) into a tab-delimited text file. Deselect any options to encapsulate fields in quotes, as extra quotes around each cell's contents might cause problems during file processing. These quotes will also inflate the file-size, so leave them out as much as possible, while also resisting any temptation to modify the xls-file by hand''. A highly-functional and free spreadsheet application can be obtained as part of the cross-platform \code{OpenOffice} suite. It works for the above required conversion. Go to \code{"http://www.openoffice.org/"}. It is regrettable that this importer does not take the xls-file directly as input. However, because of the moving-target nature of spreadsheet file formats, there is limited support for direct import of these formats into \code{R}. Rather than add to the dependency requirements of emph{phyloseq} and the relative support of these xls-support packages, it seems more efficient to choose an arbitrary delimited text format, and focus on the data structure in the PyroTagger output. This will be easier to support in the long-run. } \examples{ ## New_otuTaxObject <- import_pyrotagger_tab(pyrotagger_tab_file) } \references{ \url{http://pyrotagger.jgi-psf.org/} }